I'm very excited about this new program and think it has lots of potential. One of my main reasons for not using it yet is the lack of being able to track changes.

This is critically important in collaborative manuscript writing, not only to enable collaborators to add changes and comments/suggestions to the document, but also to create a record of author contributions.

Is this feature something we can expect to see in the future?

I also note I can't highlight anything (minor but would be great nonetheless), and when I export as a word document, I lose all the italic formatting on latin names.

Finally, I saved my test manuscript, and then we I re-opened it, it changed the title of the manuscript to the saved filename.

@HazelJ79 certainly – it may not be obvious yet from the 1.0, but collaboration has been one of the main motivations for us to build this product and we have built a lot of the technology for it already to the product that you are now using as a personal productivity tool. You'll find more discussion on the topic here: http://support.manuscriptsapp.com/topic/28/collaborative-writing/2

Annotation feature is coming up very soon. In fact the feature is already there, it's just hidden from sight as we found during the beta that it still needs more polish. Won't be long (it's actually also the basis we have for footnote support, which has been a very frequent request).